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- PDB-2c55: Solution Structure of the Human Immunodeficiency Virus Type 1 p6 ... -

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Basic information

Entry
Database: PDB / ID: 2c55
TitleSolution Structure of the Human Immunodeficiency Virus Type 1 p6 Protein
ComponentsPROTEIN P6
KeywordsVIRAL PROTEIN / P6 / HIV-1 / P6-GAG / AIDS / CORE PROTEIN / LIPOPROTEIN / MEMBRANE / METAL-BINDING / MYRISTATE / PHOSPHORYLATION / POLYPROTEIN / RNA-BINDING / VIRAL NUCLEOPROTEIN / ZINC / ZINC-FINGER
Function / homology
Function and homology information


viral budding via host ESCRT complex / ISG15 antiviral mechanism / host multivesicular body / viral nucleocapsid / host cell nucleus / host cell plasma membrane / virion membrane / structural molecule activity / RNA binding / zinc ion binding / membrane
Similarity search - Function
Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #390 / Gag protein p6 / Gag protein p6 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / gag protein p24 N-terminal domain / Helix non-globular / Special / Immunodeficiency lentiviral matrix, N-terminal / gag gene protein p17 (matrix protein) / Retroviral nucleocapsid Gag protein p24, C-terminal domain ...Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #390 / Gag protein p6 / Gag protein p6 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / gag protein p24 N-terminal domain / Helix non-globular / Special / Immunodeficiency lentiviral matrix, N-terminal / gag gene protein p17 (matrix protein) / Retroviral nucleocapsid Gag protein p24, C-terminal domain / Gag protein p24 C-terminal domain / Matrix protein, lentiviral and alpha-retroviral, N-terminal / Retrovirus capsid, C-terminal / Retroviral matrix protein / Retrovirus capsid, N-terminal / zinc finger / Zinc knuckle / Zinc finger, CCHC-type superfamily / Zinc finger, CCHC-type / Zinc finger CCHC-type profile.
Similarity search - Domain/homology
Biological speciesHUMAN IMMUNODEFICIENCY VIRUS TYPE 1
MethodSOLUTION NMR
Model type detailsMINIMIZED AVERAGE
AuthorsFossen, T. / Wray, V. / Bruns, K. / Rachmat, J. / Henklein, P. / Tessmer, U. / Maczurek, A. / Klinger, P. / Schubert, U.
CitationJournal: J.Biol.Chem. / Year: 2005
Title: Solution Structure of the Human Immunodeficiency Virus Type 1 P6 Protein.
Authors: Fossen, T. / Wray, V. / Bruns, K. / Rachmat, J. / Henklein, P. / Tessmer, U. / Maczurek, A. / Klinger, P. / Schubert, U.
History
DepositionOct 25, 2005Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 2, 2005Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PROTEIN P6


Theoretical massNumber of molelcules
Total (without water)5,8121
Polymers5,8121
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)1 / 104LEAST RESTRAINT VIOLATION
Representative

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Components

#1: Protein PROTEIN P6


Mass: 5812.297 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: P6 SEQUENCE DERIVED FROM THE ISOLATE HIV-1NL4-3 / Source: (synth.) HUMAN IMMUNODEFICIENCY VIRUS TYPE 1 / References: UniProt: P12493
Compound detailsPARTICIPATES IN BUDDING OF THE ASSEMBLED PARTICLE BY INTERACTING WITH TSG101
Sequence detailsP6 SEQUENCE DERIVED FROM THE ISOLATE HIV-1NL4-3

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111NOESY
121TOCSY
131COSY
NMR detailsText: NONE

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Sample preparation

DetailsContents: 50% WATER/50% TFE-D2
Sample conditionspH: 3.0 / Pressure: 1.0 atm / Temperature: 300.0 K

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NMR measurement

NMR spectrometerType: Bruker DMX / Manufacturer: Bruker / Model: DMX / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
CNS1BRUNGER,ADAMS,CLORE,DELANO,GROS, GROSSE- KUNSTLEVE,JIANG,KUSZEWSKI,NILGES, PANNU,READ, RICE,SIMONSON,WARRENrefinement
CNS1structure solution
RefinementSoftware ordinal: 1
Details: REFINEMENT DETAILS CAN BE FOUND IN THE JRNL CITATION ABOVE
NMR ensembleConformer selection criteria: LEAST RESTRAINT VIOLATION / Conformers calculated total number: 104 / Conformers submitted total number: 1

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